Geneious Prime version 2019.0 can import the following ﬁle formats:
|Format||Extensions||Data types||Common sources|
|Common Assembly Format||*.caf||Contigs||Sequencher|
|Clone Manager molecule||*.cm5||Sequences and annotations||Clone Manager|
|CSFASTA||*.csfasta||Color space FASTA||ABI SOLiD|
|DNAStar||*.seq, *.pro||Nucleotide & protein sequences||DNAStar|
|DNA Strider||*.str||Sequences||DNA Strider (Mac program), ApE|
|Embl/UniProt||*.embl, *.swp||Sequences||Embl, UniProt|
|EMBOSS codon usage table||*.cusp, *.cut||Codon usage table||EMBOSS cusp tool|
|Endnote (8.0 or 9.0) XML||*.xml||Journal article references||Endnote, Journal article websites|
|FASTA||*.fasta, *.fas, *fasta.gz etc.||Sequences, alignments||PAUP*, ClustalX, BLAST, FASTA|
|FASTQ||*.fastq, *.fq, *fastq.gz etc.||Sequences with quality||Illumina and other NGS sequencers|
|GCG codon usage table||*.cod||Codon usage table||GCG CodonFrequency tool, https://www.kazusa.or.jp/codon/|
|GenBank||*.gb, *.xml||Nucleotide & protein sequences||GenBank|
|Geneious||*.xml, *.geneious||Preferences, databases||Geneious|
|Geneious Education||*.tutorial.zip||Tutorial, assignment etc.||Geneious|
|GFF, GFF3, GTF||*.gﬀ, *.gﬀ3, *.gtf||Annotations||NCBI, Ensembl and other genome browsers|
|Molecular structure||*.pdb, *.mol, *.xyz, *.cml,|
|*.gpr, *.hin, *.nwo||3D molecular structures||3D structure databases and programs|
|Newick||*.tre, *.tree, etc.||Phylogenetic trees||PHYLIP, Tree-Puzzle, PAUP*, ClustalX|
|Nexus||*.nxs, *.nex||Trees, Alignments||PAUP*, Mesquite, MrBayes & MacClade|
|PDB||*.pdb||3D Protein structures||SP3, SP2, SPARKS, Protein Data Bank|
|Documents, presentations||Adobe Writer, LATEX, Miktex|
|Phrap ACE||*.ace||Contig assemblies||Phrap/Consed|
|PIR/NBRF||*.pir||Sequences, alignments||NBRF PIR|
|Qual||*.qual||Quality ﬁle||Associated with a FASTA ﬁle|
|Raw sequence text||*.seq||Sequences||Any ﬁle that contains only a sequence|
|Rich Sequence Format||*.rsf||Sequences, alignments||GCGs NetFetch|
|Comma/Tab Separated Values||*.csv, *.tsv||Spreadsheet ﬁles||Microsoft Excel|
|Sequence Chromatograms||*.ab1, *.scf||Raw sequencing trace & sequence||Sequencing machines|
|SnapGene sequence||*.dna||Sequences and annotations||SnapGene|
|Text/html||.txt, .rtf, .html||Any text||Simple text editors|
|VCF||*.VCF||Annotations||1000 Genomes Project|
|Vector NTI sequence||*.gb, *.gp||Nucleotide & protein sequences||Vector NTI|
|Vector NTI/AlignX alignment||*.apr||Alignments||Vector NTI, AlignX|
|Vector NTI Archive||*.ma4, *.pa4, *.oa4,||Nucleotide & protein sequences,|
|*.ea4, *.ca6||enzyme sets and publications||Vector NTI|
|Vector NTI/ContigExpress||*.cep||Nucleotide sequence assemblies||Vector NTI|
|Vector NTI database||VNTI Database||Nucleotide & protein sequences,|
|enzyme sets and publications||Vector NTI|
The BED format contains sequence annotation information. You can use a BED ﬁle to annotate existing sequences in your local database, import entirely new sequences, or import the annotations onto blank sequences.
Geneious can import annotated sequences ﬁles in the standard Clone Manager molecule format .cm5. This will import name, description, topology, sequence and annotations. Currently it does not import other ﬁelds, restriction cut sites or primer binding sites.
Other Clone Manager formats such as .cx5 and .pd4 are not currently supported for import.
The Clustal format is used by ClustalW and ClustalX, two well known multiple sequence alignment programs.
Clustal format ﬁles are used to store multiple sequence alignments and contain the word clustal at the beginning. An example Clustal ﬁle:
ABI .csfasta ﬁles represent the color calls generated by the SOLiD sequencing system.
DNAStar .seq and .pro ﬁles are used in Lasergene, a sequence analysis tool produced by DNAStar.
Sequence ﬁles generated by the Mac program DNA Strider, containing one Nucleotide or Protein sequence.
Nucleotide sequences from the EMBL Nucleotide Sequence Database, and protein sequences from UniProt (the Universal Protein Resource)
EndNote is a popular reference and bibliography manager. EndNote lets you search for journal articles online, import citations, perform searches on your own notes, and insert references into documents. It also generates a bibliography in diﬀerent styles. Geneious can interoperate with EndNote using Endnote’s XML (Extensible Markup Language) ﬁle format to export and import its ﬁles.
The FASTA ﬁle format is commonly used by many programs and tools, including BLAST, T-Coﬀee and ClustalX. Each sequence in a FASTA ﬁle has a header line beginning with a “>” followed by a number of lines containing the raw protein or DNA sequence data. The sequence data may span multiple lines and these sequence may contain gap characters. An empty line may or may not separate consecutive sequences. Here is an example of three sequences in FASTA format (DNA, Protein, Aligned DNA):
FASTQ format stores sequences and Phred qualities in a single ﬁle. These should typically be used to import NGS sequence data e.g from Illumina, Ion Torrent, 454 and PacBio sequencers. From R11 onwards, you can set read technology and pair reads as part of the Fastq import process. Note that the native HDF5 ﬁle format from PacBio and Oxford Nanopore is not supported and must be converted to fastq for import into Geneious.
Records retrieved from the NCBI website (http://www.ncbi.nlm.nih.gov) can be saved in a number of formats. Records saved in GenBank or INSDSeq XML formats can be imported into Geneious.
The Geneious format can be used to store all your local documents, meta-data types and program preferences. A ﬁle in Geneious format will usually have a .geneious extension or a .xml extension. This format is useful for sharing documents with other Geneious users and backing up your Geneious data.
This is an archive containing a whole bundle of ﬁles which together comprise a Geneious education document. This format can be used to create assignments for your students, bioinformatics tutorials, and much more. See chapter 17 for information on how to create such ﬁles.
The GFF format contains sequence annotation information (and optional sequences). You can use a GFF ﬁle to annotate existing sequences in your local database, import entirely new sequences, or import the annotations onto blank sequences. Geneious also supports GFF3 and GTF formats.
The MEGA format is used by MEGA (Molecular Evolutionary Genetics Analysis).
Geneious imports a range of molecular structure formats. These formats support showing the locations of the atoms in a molecule in 3D:
The Newick format is commonly used to represent phylogenetic trees (such as those inferred from multiple sequence alignments). Newick trees use pairs of parentheses to group related taxa, separated by a comma (,). Some trees include numbers (branch lengths) that indicate the distance on the evolutionary tree from that taxa to its most recent ancestor. If these branch lengths are present they are preﬁxed with a colon (:). The Newick format is produced by phylogeny programs such as PHYLIP, PAUP*, Tree-Puzzle and PHYML. Geneious can import and export trees (including bootstrap values and branch lengths) in Newick format.
The Nexus format was designed to standardize the exchange of phylogenetic data, including sequences, trees, distance matrices and so on. The format is composed of a number of blocks such as TAXA, TREES and CHARACTERS. Each block contains pre-deﬁned ﬁelds. Geneious imports and exports ﬁles in Nexus format, and can process the information stored in them for analysis.
If you want to export a tree in a format that preserves bootstrap values make sure you export with metacomments enabled, otherwise the bootstraps will be lost.
Protein Databank ﬁles contain a list of XYZ co-ordinates that describe the position of atoms in a protein. These are then used to generate a 3D model which is usually viewed with Rasmol or SPDB viewer. Geneious can read PDB format ﬁles and display an interactive 3D view of the protein structure, including support for displaying the protein’s secondary structure when the appropriate information is available.
PDF stands for Portable Document Format and is developed and distributed by Adobe Systems. It contains the entire description of a document including text, fonts, graphics, colors, links and images. The advantage of PDF ﬁles is that they look the same regardless of the software used to create them. Some word processors are able to export a document into PDF format. Alternatively, Adobe Writer can be used. You can use Geneious to read, store and open PDF ﬁles.
Ace is the format used by the Phrap/Consed package, created by the University of Washington Genome Center. This package is used mainly to assemble sequences.
The PileUp format is used by the pileup program, a part of the Genetics Computer Group (GCG) Wisconsin Package.
Format used by the Protein Information Resource, a database established by the National Biomedical Research Foundation
Quality ﬁle which must be in the same folder as the sequence ﬁle (FASTA format) for the quality scores to be used.
A ﬁle containing only a sequence.
RSF (Rich Sequence Format) ﬁles contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information.
Sequences such as primer lists are often stored in spreadsheets. Geneious has an importer that can be given the ﬁeld values for a spreadsheet ﬁle exported in CSV or TSV format, and it will import them and convert them to documents as well as preserving the additional ﬁeld contents. It can handle nucleotide and protein sequences, as well as primers and probes. For more information on importing primers from a spreadsheet, see the PCR Primers section.
SAM and BAM format are produced and used by SAMtools. SAM/BAM ﬁles contain the results of an assembly in the form of reads and their mappings to reference sequences.
Sequence chromatogram documents contain the results of a sequencing run (the trace) and a guess at the sequence data (base calling).
Informally, the trace is a graph showing the concentration of each nucleotide against sequence positions. Base calling software detects peaks in the four traces and assigns the most probable base at more or less even intervals.
Geneious can import annotated DNA sequence ﬁles in .dna format from SnapGene. Note that for sequences longer than 65,536 bases, restriction sites are not imported automatically, but you will be asked if you wish to import them as an enzyme set. You can then re-annotate the sites onto the sequence using “Find restriction sites”.
Plain text ﬁles and simple HTML can be imported and displayed. HTML is a widely used markup language that can apply format and structure to text, and will be interpreted by the sequence viewer. In Geneious R10 and above, text ﬁles can also be created and edited in Geneious, see section 4.1.4 .
The VCF format contains sequence annotation information. You can use a VCF ﬁle to annotate existing sequences in your local database, import entirely new sequences, or import the annotations onto blank sequences.
Geneious supports the import of several Vector NTI formats: